We are pleased to introduce version 12.6 of our ChemDoodle 2D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $19, and we have a free trial available at: https://www.chemdoodle.com/


Some new features in ChemDoodle 2D v12.6.

Executive Summary

Version 12.6.0 is a feature update for ChemDoodle 2D. Included are new features for EPS file output, new keyboard and tool actions familiar to experienced chemists, a new solubility calculator, the ability to organize content by selections of atoms, and more.


  1. Alignment, distribution and centering may now be performed on selections of atoms, instead of the whole molecules they are a part of. This will make it much easier to organize figures based on individual atoms within structures. Please see section 11.4 of the ChemDoodle user guide for further instructions.
  2. Improved perspective structure automatic z-ordering with another geometry type.
  3. Added a solubility (logS) calculator based on the Hou algorithm, which can be accessed in the Structure>Descriptors menu, in the Properties widget, and as an auto-updating label.
  4. Condensed labels ending in a radical formula (i.e. OC2H5) are now supported.
  5. Support added for SO3H abbreviation.
  6. When editing text components (atom label or caption), the return/enter key will now confirm and set the text object, while using control+return or control+enter will add a new line. Escape will now cancel and revert the text object to the previous state.
  7. Using the "z" key to flip curved arrows with fishhook end arrowheads will now move the fishhook to the opposite side of that end of the line.
  8. Pressing the system meta key (control on Windows/Linux, command on macOS) and dragging selected content will now duplicate that content. You may also press the system meta key while transforming selected content to copy the current state of that selected content. Use this method to stamp copies of your selected content as you transform it. Please see section 11.3 of the ChemDoodle user guide for further instructions.
  9. Double clicking on an atom or bond using a selection tool will now default to selecting the entire molecule. You may change this behavior back to editing the styles of the object in the Controls settings, by changing the Double Click on Atom/Bond setting.
  10. There are now options in Save Settings to disable the individual output settings window for chemical file and image output, when using the Save/Save As... functions. If disabled, the default settings will be applied. Chemical file settings windows are now provided on save, but are disabled by default.
  11. The Chemical Files settings panel has been reorganized for clarity.
  12. EPS output now includes an option to preserve chemnum tags in output. Such chemnum tags are defaulted as "TMPx", but you may change what the chemnum tag is to be used. These tags, when written in caption labels, will be preserved as unbroken text in EPS output, even if the Render Text as Shapes option is enabled. This way, you can work with chemnum and still have perfect font glyph output to EPS files for your figures.
  13. Bitmap image output is now supported in EPS files.
  14. Bitmap images copied to the system clipboard now adhere to the default application settings for images (scale, resolution, etc.).
  15. Images are now rendered on the fly at the correct native resolution of the image, fixing output scaling issues. Progressive bilinear scaling has been removed.
  16. The precisionFDA integration now has its own submenu in the File>Interfaces submenu. Simply select a structure and then select the precisionFDA>UNIISearch menu item to execute a search. Please see Appendix A.12 of the ChemDoodle user guide for further instructions.


  1. Corrected minor tetrahedral stereochemistry perception edge case.
  2. Setting enhanced stereochemistry to an atom now stops the stereochemistry menu from showing options when right clicking on that atom.
  3. Assigning stereochemical configurations for a structure with enhanced stereochemistry present now disregards enhanced stereocenters.
  4. Fixed issue where stereochemical functions were not showing in the context menu and the Structure>Stereochemistry>Resolve functions did not have any effect for centers that are spiro and symmetrical.
  5. Hydrogens connected by a single bond to a chiral center are now removed by the remove hydrogens functions. Only wedge connected hydrogens will be retained on stereocenters.
  6. Added a clearer error message when trying to force a stereo configuration in a projection, when no correct orientation is possible.
  7. Resolved error generating traditional IUPAC names with multiple isotopes.
  8. Hiding a carbon label will now work on carbon atoms when the implicit hydrogen count has been defined to 0.
  9. Undo and redo of the show/hide carbon label action has been corrected to revert back to the previous state of the atom.
  10. The center and distribute on page functions will now keep selected content within the page the center of that content is present on.
  11. Corrected issue when fixed bond angles is disabled and then adding an aromatic ring on using the alt+6 keyboard shortcut lead to a weirdly attached angle.
  12. Corrected a bug where setting a manual attribute wasn't working.
  13. Double click when hovering on a shape in a shape state now opens the styles window for that shape.
  14. Fixed issue where SMILES output does not properly include explicit hydrogens for stereocenters if the option to write explicit hydrogens is enabled.
  15. PDB, PDBML, BCIF, MMCIF and MMTF filetypes all now use the same compatibility warning setting.
  16. Corrected EPS output encoding to enable support of more character glyphs.
  17. For clarity, the "2D Stochastic Build" menu item has been renamed to "Beautify Structure Drawing".
  18. Prevented keyboard tool shortcuts from executing when completing some menu accelerator commands.
  19. Provided a workaround on macOS to reenable the menu bar after the file dialog has been closed without leaving the application.
  20. Provided a workaround for an error in PowerPoint on Windows, where a round-trip copy of an OLE object into PowerPoint and back into ChemDoodle doesn't work.